A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

Background The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. Findings This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families. Conclusions This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.

Adults have more male-biased sex ratios than first-winter juveniles in wintering duck populations

Background The long-term monitoring of demographic changes in waterbird populations remains limited, but such information can be valuable for conservationists and waterbird managers. Biased sex ratios can indicate differences in survival rates between sexes. In particular, differences in the sex ratios of fledged juveniles and adults can provide insight into the development of male bias among populations. Methods In this study, we used data from individual birds captured over a 57-year period to assess the extent, and temporal variability in male bias in nine populations of ducks wintering in the United Kingdom: Gadwall (Mareca strepera), Northern Mallard (Anas platyrhynchos), Northern Pintail (Anas acuta), Common Pochard (Aythya ferina), Common Shelduck (Tadorna tadorna), Northern Shoveler (Spatula clypeata), Eurasian Teal (Anas crecca), Tufted Duck (Aythya fuligula), and Eurasian Wigeon (Mareca penelope). Results Overall, eight of these populations were significantly male-biased and adults were more male-biased than first-winter juveniles for all nine populations. The increased male bias among adults is consistent with the hypothesis that factors such as higher mortality of reproductive-age females during the breeding season is a major cause of male bias in duck populations. However, such predation cannot explain the male bias detected in first-winter juveniles in four of the populations. The temporal trends in male bias differed between adults and first-winter juveniles in Northern Mallard, Northern Pintail, Common Pochard, Common Shelduck, Eurasian Teal, Tufted Duck, and Eurasian Wigeon. Over the study period we found increased male bias among adult Northern Mallard, Northern Pintail, Common Pochard, Common Shelduck, and Tufted Duck as well as both adult and first-winter juvenile Northern Shoveler. Conclusions We provide evidence that among wintering duck populations, sex ratios are typically male-biased, with adults exhibiting stronger male-biased sex ratios than first-winter juveniles. Improved monitoring of sex ratios of wintering waterbirds would help to increase our understanding of changes in waterbird demography, population structure, and observed population trends; our study shows that birds caught during ringing projects can be a valuable source of such data.

Changes in numbers and distribution of wintering waterbirds around Gotland 1969–2020

The coastal areas of the island of Gotland in the center of the Baltic Sea is an important wintering site for waterbirds in Sweden. Gotland offers extensive areas of shallow feeding grounds and, due to its location, some open waters remain available even during harsh winters. Wintering waterbirds have been counted annually on the island since the start of the International Waterbird Census in 1967, with full coverage of all the inshore areas around the main island obtained during the years 1969–1978 and 2013–2020. Between these two periods, the mean total number of wintering waterbirds increased from 32,000 to 111,500. The most numerous species were Mallard Anas platyrhynchos, Tufted Duck Aythya fuligula, and Common Goldeneye Bucephala clangula. Some species such as Eurasian Wigeon Mareca penelope, Eurasian Teal Anas crecca, and Gadwall Mareca strepera started to winter during the second period. Marked increases were also found for Smew Mergellus albellus and Greater Scaup Aythya marila, likely related to progressively milder winters in recent years.

A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck)

BackgroundThe tufted duck is a non-model organism that suffers high mortality in highly pathogenic avian influenza out-breaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.ResultsThis study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (cDNA) from brain, ileum, lung, ovary, spleen and testis using Illumina short-read and PacBio long-read sequencing platforms, which was used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies an average of 7.9 isoforms per gene. We also identified 246 small RNA families.ConclusionsThis annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to the avian influenza virus.

MIGRATORY WETLAND BIRDS DIVERSITY IN LOWER CHOTA NAGPUR PLATEAU WITH SPECIAL REFERENCE TO PURULIA DISTRICT, WEST BENGAL, INDIA

Lower Chota Nagpur Plateau has several large and small water bodies having diverse aquatic flora and fauna. These wetlands not only provide suitable habitat for resident and as well as migratory avian species but also contribute much to the biodiversity. The present study deals with the diversity, abundance and variations of avian migratory species at wetlands of Purulia district. The study reflects that there are 43 migratory bird species in number in these wetland regions belonging to 8 orders and 12 families. Red-crested Pochard, Tufted Duck, Lesser Whistling Duck, Northern Pintail, Gadwall, Eurasian Wigeon, Common Coot etc. are found in large number in winter season in these wetlands.

Serological Evidence of West Nile Virus in Wild Birds in Bangladesh

West Nile Virus (WNV) is a vector-borne zoonotic disease maintained in a sylvatic cycle involving mosquito vectors and birds. To detect WNV and other flavivirus infections in wild resident and migratory birds, we tested 184 samples from 19 identified species within nine families collected during 2012–2016 from four districts in Bangladesh. We tested serum samples for the immunoglobulin G (IgG) antibody against WNV using competitive Enzyme-Linked Immunosorbent Assay (c-ELISA), whereas tracheal and cloacal swabs were subjected to consensus Polymerase Chain Reaction (c-PCR) for the detection of the flavivirus RNA. Overall, we detected 11.9% (n = 22; 95% CI: 0.07–0.16) samples were seropositive, including 15.9% in the migratory wild birds and 10.7% in the resident wild birds. The migratory wild Tufted duck showed 28.5% seropositivity, whereas the resident wild house crows showed 12.5% seropositivity. None of the swab samples was positive for flavivirus RNA infection (0%, n = 184; 95% CI: 0–0.019). These study findings recommend continued surveillance for early detection and to better understand the epidemiology of WNV and other flavivirus circulation in both birds and mosquitoes in Bangladesh.

Changes in numbers and distribution of wintering waterbirds at the south coast of Scania, Sweden, during 55 winters, 1964–2018

The south coast of Scania, southernmost Sweden, has long been an important wintering and staging area for waterbirds. A large part of the coast was surveyed annually as a part of the international midwinter counts for 55 years (1964–2018). The total number of wintering waterbirds showed an increasing trend but there was much variation between years. Common Goldeneye Bucephala clangula, followed by Mallard Anas platyrhynchos, Tufted Duck Aythya fuligula and—during the early years—Long-tailed Duck Clangula hyemalis, dominated the community. Great Cormorant Phalacrocorax carbo, Mallard, Common Goldeneye and Eurasian Coot Fulica atra increased in numbers, reflecting the national and international trends related to milder winters and a northward shift of the winter distribution. Eurasian Wigeon Mareca penelope and Great Crested Grebe Podiceps cristatus established wintering traditions in the area during the study period. Tufted Duck and Common Merganser Mergus merganser decreased locally due to a northward shift of the wintering distribution northwards within the country. The Long-tailed Duck was an important winter guest in the first years but was only seen in very small numbers in later years, reflecting the general and large-scale decrease of the Baltic wintering population.

Waterbird counts on large water bodies: comparing ground and aerial methods during different ice conditions

The aerial and ground methods of counting birds in a coastal area during different ice conditions were compared. Ice coverage of water was an important factor affecting the results of the two methods. When the water was ice-free, more birds were counted from the ground, whereas during ice conditions, higher numbers were obtained from the air. The first group of waterbirds with the smallest difference between the two methods (average 6%) contained seven species: Mute Swan Cygnus olor, Whooper Swan Cygnus cygnus, Greater Scaup Aythya marila, Tufted Duck Aythya fuligula, Common Goldeneye Bucephala clangula, Smew Mergellus albellus and Goosander Mergus merganser; these were treated as the core group. The second group with a moderate difference (average 20%) included another six species: Mallard Anas platyrhynchos, Eurasian Wigeon Mareca penelope, Common Pochard Aythya ferina, Great Crested Grebe Podiceps cristatus and Eurasian Coot Fulica atra. The third group with a large difference (average 85%) included five species, all of the Anatini tribe: Gadwall Mareca strepera, Northern Pintail Anas acuta, Northern Shoveler Spatula clypeata, Eurasian Teal Anas crecca and Garganey Spatula querquedula. During ice conditions, smaller numbers of most species were counted from the ground. The exception here was Mallard, more of which were counted from the ground, but the difference between two methods was relatively small in this species (7.5%). Under ice-free conditions, both methods can be used interchangeably for the most numerous birds occupying open water (core group) without any significant impact on the results. When water areas are frozen over, air counts are preferable as the results are more reliable. The cost analysis shows that a survey carried out by volunteer observers (reimbursement of travel expenses only) from the land is 58% cheaper, but if the observers are paid, then an aerial survey is 40% more economical.

Waterbird counts on large water bodies: comparing ground and aerial methods during different ice conditions

The paper compares the aerial and ground methods of counting birds in a coastal area during different ice conditions. Ice coverage of waters was the most important factor affecting the results of the two methods. When the water was ice-free, more birds were counted from the ground, whereas during ice conditions, higher numbers were obtained from the air. In ice-free conditions the group of waterbirds with the smallest difference between the two methods (< 6%) contained six species: Greater Scaup, Smew, Mute Swan, Goosander, Common Goldeneye and Tufted Duck; the group with a moderate difference (15%-45%) included another six species: Eurasian Coot, Whooper Swan, Mallard, Eurasian Wigeon, Great Crested Grebe and Common Pochard; while the group with a large difference (> 68%) included five species, all of the genus Anas: Gadwall, Eurasian Teal, Northern Shoveler, Northern Pintail and Garganey. In ice conditions, smaller numbers of most species were counted from the ground, except for Mallard, where the difference between two methods was small (7.5%). Under ice-free conditions, both methods can be used interchangeably for the most numerous birds occupying open water without any great impact on the results. When water areas are frozen over, air counts are preferable as the results are more accurate. The cost analysis shows that a survey carried out by volunteer observers (reimbursement of travel expenses only) from the land is 58% cheaper, but if the observers are paid, then the aerial survey is 40% more economical.